Transfer of Antibiotic Resistance Plasmid from Commensal E. coli Towards Human Intestinal Microbiota in the M-SHIME: Effect of E. coli dosis, Human Individual and Antibiotic Use

Establishment of a Low-Cost and Efficient In Vitro Model for Cultivating Intestinal Microbiota

The Simulator of Human Intestinal Microbial Ecosystem (SHIME) has hindered widespread adoption due to its high cost. This study founded biomimetic multilink fermentation equipment (BMLFE), priced at half or even lower than SHIME. It was improved based on multilink fermentation equipment (MLFE) by modifying materials, peristaltic pumps, fermentation time, and dietary habits while calculating transfer time and volumes and conducted anaerobic fermentation for 15 days followed by monitoring changes in intestinal microbial composition and short-chain fatty acids (SCFAs). We observed that the intestinal microbiota achieved a stable state after the ninth day and retained the predominant bacterial species in the fecal inoculum. The Bacillota/Bacteroidota values of the descending colon (DC) were similar to those in the fecal samples. However, the stability of SCFAs was relatively delayed and reached stability only after the 11th day. Meanwhile, the concentration ratio of acetic acid, propionate, and butyric acid metabolized by transverse colon (TC) and DC on the 11-15th days was close to that in fecal inoculations. Therefore, BMLFE can be used to simulate the human gastrointestinal environment in vitro studies. It is expected to be employed in clinical FMT and may even contribute to establishing stable enterotypes through dietary intervention.

Effects of prebiotics from diverse sources on dysbiotic gut microbiota associated to western diet: Insights from the human Mucosal ARtificial COLon (M-ARCOL)

Associated to various illnesses, Western Diet (WD) is acknowledged to have deleterious effects on human gut microbiota, decreasing bacterial diversity, lowering gut bacteria associated to health (such as Akkermansia muciniphila), while increasing those linked to diseases (e.g., Proteobacteria). In this study, we evaluated the potential of two new prebiotics to counteract the negative effect of WD on gut microbiota, namely raffinose family oligosaccharides (RFO) from chickpeas and laminarin (LAM) from algae, when compared to the well-known inulin (INU). The effects of prebiotics on gut microbiota composition and metabolic activities were investigated in the Mucosal-Artificial Colon, set-up to reproduce WD condition, as compared to healthy control (n = 3). None of the prebiotics was able to efficiently offset the shift in microbiota induced by WD. Nevertheless, when compared to non-supplemented WD, all prebiotics showed significant impacts on microbiota composition, that were both prebiotic and donor-dependant. RFO was the only prebiotic to enhance α-diversity, while it led to an increase in Blautia and Butyricicoccaceae, associated with higher amounts of gas and butyrate. LAM and INU did not strongly impact microbial metabolic activities but were associated with a rise in Prevotella_9/Agathobacter and Faecalibacterium, respectively. To conclude, this study showed that all tested prebiotics had different impacts on human gut microbiota structure and activities, which was further donor-dependent. M-ARCOL appears as a suitable in vitro tool to better understand the mechanisms of action of prebiotic compounds in relation to gut microbes and define responders and non-responders to prebiotic supplementation, opening the possibility of customized nutritional strategies.

Simulator of the Human Intestinal Microbial Ecosystem (SHIME®): Current Developments, Applications, and Future Prospects

The human gastrointestinal microbiota plays a vital role in maintaining host health and preventing diseases, prompting the creation of simulators to replicate this intricate system. The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), a multicompartment dynamic simulator, has emerged as a pivotal in vitro model for studying the interactions and interferences within the human gut microbiota. The continuous and real-time monitoring hallmarks, along with the programmatically flexible setup, bestow SHIME® with the ability to mimic the entire human intestinal ecosystem with high dynamics and stability, allowing the evaluation of various treatments on the bowel microbiota in a controlled environment. This review outlines recent developments in SHIME® systems, including the M-SHIME®, Twin-SHIME®, Triple-SHIME®, and Toddle SHIME® models, highlighting their applications in the fields of food and nutritional science, drug development, gut health research, and traditional Chinese medicine. Additionally, the prospect of SHIME® integrating with other advanced technologies is also discussed. The findings underscore the versatility of SHIME® technology, demonstrating its significant contributions to current gut ecosystem research and its potential for future innovation in microbiome-related fields.

Cultivating complexity: Advancements in establishing in vitro models for the mucus-adhering gut microbiota

A healthy mucus is essential for maintaining intestinal homeostasis and overall well-being. In recent years, extensive research focused on understanding the intricate interactions between mucus and the gut microbiota. Mucus-adhering bacteria play crucial roles in preserving barrier integrity, epithelial permeability and mucus architecture, as well as in the colonization resistance against pathogens. Unravelling the significance of these microorganisms in human health and disease is challenging, primarily because most of the studies on the human gut microbiota rely on faecal samples, which do not fully represent the microecological complexity found in the intestinal mucosa. This review discusses novel strategies to specifically target and evaluate the mucosal microbiota, such as culturomics applied to mucosal biopsies or brushings, intestinal organoids and artificial in vitro models incorporating mucus.

In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome

Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.

Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011-2017)

Salmonella Kentucky is commonly found in poultry and rarely associated with human disease. However, a multidrug-resistant (MDR) S. Kentucky clone [sequence type (ST)198] has been increasingly reported globally in humans and animals. Our aim here was to assess if the recently reported increase of S. Kentucky in poultry in Spain was associated with the ST198 clone and to characterize this MDR clone and its distribution in Spain. Sixty-six isolates retrieved from turkey, laying hen and broiler in 2011–2017 were subjected to whole-genome sequencing to assess their sequence type, genetic relatedness, and presence of antimicrobial resistance genes (ARGs), plasmid replicons and virulence factors. Thirteen strains were further analysed using long-read sequencing technologies to characterize the genetic background associated with ARGs. All isolates belonged to the ST198 clone and were grouped in three clades associated with the presence of a specific point mutation in the gyrA gene, their geographical origin and isolation year. All strains carried between one and 16 ARGs whose presence correlated with the resistance phenotype to between two and eight antimicrobials. The ARGs were located in the Salmonella genomic island (SGI-1) and in some cases (bla_SHV-12, catA1, cmlA1, dfrA and multiple aminoglycoside-resistance genes) in IncHI2/IncI1 plasmids, some of which were consistently detected in different years/farms in certain regions, suggesting they could persist over time. Our results indicate that the MDR S. Kentucky ST198 is present in all investigated poultry hosts in Spain, and that certain strains also carry additional plasmid-mediated ARGs, thus increasing its potential public health significance.

Shewanella algae and Morganella morganii Coinfection in Cobra-Bite Wounds: A Genomic Analysis

Naja atra bites cause severe soft tissue injury and are prone to wound infections. The pathogens of Naja atra bite-wound infections are highly variable in different geographical regions. Here, we report the first coinfection with Shewanella algae and Morganella morganii from a Naja atra bite wound with resistome analysis using whole genome sequencing.